In this study, we investigated the emergence of spatial self-organized patterns on intertidal flats, resulting from the interaction between biological and geomorphological processes. Autocorrelation analysis of aerial photographs revealed that diatoms occur in regularly spaced patterns consisting of elevated hummocks alternating with water-filled hollows. Hummocks were characterized by high diatom content and a high sediment erosion threshold, while both were low in hollows. These results highlight the interaction between diatom growth and sedimentary processes as a potential mechanism for spatial patterning. Several alternative mechanisms could be excluded as important mechanisms in the formation of spatial patterns. We developed a spatially explicit mathematical model that revealed that scale-dependent interactions between sedimentation, diatom growth, and water redistribution explain the observed patterns. The model predicts that areas exhibiting spatially self-organized patterns have increased sediment accretion and diatom biomass compared with areas lacking spatial patterns, a prediction confirmed by empirical evidence. Our study on intertidal mudflats provides a simple but clear-cut example of how the interaction between biological and sedimentary processes, through the process of self-organization, induces spatial patterns at a landscape level.